So far Emacs has been, for many users, nice abstraction over the OS. As soon as I'm not able to use the same packages and have the same setup on both Linux and Windows, I won't use it anywhere and start looking at the alternatives.
The purpose of this is not to limit functionality to a specific platform, it's to expand the capabilities of Emacs. My understanding is FFI is intended to work on all platforms that Emacs support, so it just means the library authors need to provide platform specific support, just the same as they do with packages that depend on specific binaries in the path.
Throwing out a new feature that provides obvious benefits because of imagined future packages that may choose against being platform agnostic seems rather short sighted.